title: Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.
abstract: Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA. bmhenn@stanford.edu
authors.forename: Brenna M
authors.initials: BM
authors.lastname: Henn
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Gignoux
authors.forename: Matthew
authors.initials: M
authors.lastname: Jobin
authors.forename: Julie M
authors.initials: JM
authors.lastname: Granka
authors.forename: J M
authors.initials: JM
authors.lastname: Macpherson
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Kidd
authors.forename: Laura
authors.initials: L
authors.lastname: Rodríguez-Botigué
authors.forename: Sohini
authors.initials: S
authors.lastname: Ramachandran
authors.forename: Lawrence
authors.initials: L
authors.lastname: Hon
authors.forename: Abra
authors.initials: A
authors.lastname: Brisbin
authors.forename: Alice A
authors.initials: AA
authors.lastname: Lin
authors.forename: Peter A
authors.initials: PA
authors.lastname: Underhill
authors.forename: David
authors.initials: D
authors.lastname: Comas
authors.forename: Kenneth K
authors.initials: KK
authors.lastname: Kidd
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Norman
authors.forename: Peter
authors.initials: P
authors.lastname: Parham
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Mountain
authors.forename: Marcus W
authors.initials: MW
authors.lastname: Feldman
mesh_terms: D000349:Africa; D005075:Biological Evolution; D044383:Black People / Q000235:genetics*; D003469:Culture; D005006:Ethnicity / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide